Here's what we know: the MTA is applying for $4.5 billion in federal funds to fortify New York's transit system against future storms. What we don't yet know: will the authority figure out how to to seal off the mouths of the 14 tubes that lie beneath the city's waterways?

The question is vital because without the ability to prevent catastrophic flooding in those tubes, all the authority's restoration work could, in another storm, be washed away.

On Wednesday, officials unveiled a variety of options including inflatable plugs to seal off subway tunnels and closing off subway entrances -- there are 540 openings in Lower Manhattan alone.

MTA head Thomas Prendergast, along with Housing & Urban Development Secretary Shaun Donovan and Governor Andrew Cuomo, inspecting a removable subway stair flood control cover at the Whitehall St. Station/Marc Hermann, MTA

At a press conference Tuesday, Governor Cuomo conceded that the designs are "experimental" and the funding isn't yet in place. "I don’t have a price on the plugs," Cuomo told reporters. "This is an experimental design they were working on. And if the MTA thinks it works we'll take it to the next level. But for sure we have to seal off the subway system and there are a number of devices to do that. We saw metal hatches, -- that's one way to do it. covers from the top, the inflatable bladders in the subway, but you have to keep water from filling the system. That's a priority,"

"And the MTA will get help from you, on the capital program, for that?" the Governor was asked.

"The MTA gets whatever they want. Whatever Tom Prendergast wants, he just asks. "Cuomo said, jokingly. "This is one of the rare occasions where the question, the issue is not about funding. Because the federal government was supportive. The president was personally supportive, and the congress passed a supplemental appropriation that I believe is going to be appropriate to fill all these needs. So that's the good news. It’s not going to be about money, it’s going to be about technology. This is a massive undertaking, when you think of the subways alone, and trying to close every opening."

The Federal Transit Administration called it the worst transit disaster in American history.

Some of the comeback was quick: 80 percent of subway service was restored within a week. But riders are still dealing with Sandy damage. The major part of South Ferry subway station is closed, and will be for years. And the 65,000 weekday riders of the R train are painfully aware that the Montague tube, which carries their train from Brooklyn to Manhattan, is closed for a 14-month repair job. Part of the G train is shut down on weekends for similar repairs.

And now, as is the case once a year, we're in another hurricane season.

NY Governor Cuomo (blue tie)/Jim O'Grady, WNYC

The MTA has said it will cost nearly $5 billion to get the MTA back to where it was before Sandy. And another $4 billion to harden the system. So $9 billion all together -- almost all it coming from the federal government's Sandy relief fund. The MTA has an entire division devoted to fixing and fortifying the subway and commuter lines. It's going to take several more years at least.

The MTA has built a seawall in the Rockaways to protect the A train. In the Montague tube and other places, they're wrapping electrical cables with insulation that protects against salt water. Those are two among countless improvements to the system. But the authority -- and New York City -- will still have a major problem if the tubes flood. The MTA can raise all the signals it wants, but if even a foot of water enters a tube, there is still a big problem. That problem is the third rail, which can't be raised. Transit workers will tell you that once a third rail is coated with saltwater, which conducts electricity, that rail is ruined and needs to be replaced...at great expense.

Until Tuesday, the MTA and the Governor were tight-lipped. But Senator Charles Schumer had no problem floating the idea at a recent press conference on the Brooklyn waterfront about Sandy recovery funding.

"They will, depending on the tunnel, find ways to block entrances with giant airbags, gates or whatever that can quickly close," he said.

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